Academic Commons Search Resultshttp://academiccommons.columbia.edu/catalog.rss?f%5Bdepartment_facet%5D%5B%5D=Radiation+Oncology&f%5Bsubject_facet%5D%5B%5D=Medical+imaging+and+radiology&q=&rows=500&sort=record_creation_date+desc
Academic Commons Search Resultsen-usStructure-Function Relationships in the Human Visual System Using DTI, fMRI and Visual Field Testing: Pre- and Post-Operative Assessments in Patients with Anterior Visual Pathway Compressionhttp://academiccommons.columbia.edu/catalog/ac:177044
Rosiene, J.; Liu, X.; Imielinska, Celina Z.; Ferrera, J.; Bruce, J.; Hirsch, Joy; D'Ambrosio, A.http://dx.doi.org/10.7916/D8445JZQTue, 09 Sep 2014 00:00:00 +0000The recently developed magnetic resonance technique of diffusion tensor imaging (DTI), is used clinically to trace the structure of white fiber tracts in the human brain. This novel imaging technique that derives microstructural and physiological features of tissues has many potential immediate practical applications. The focus of this paper is to improve our understanding of the relationships between brain structure and function, using pre- and post-operative assessment in patients with anterior visual pathway compression.Bioinformatics, Medical imaging and radiology, Neurosciencesci42Radiation Oncology, Neurological Surgery, Biomedical Informatics, Functional Magnetic Resonance Imaging Research CenterReportsEnhanced Techniques for Asymmetry Quantification in Brain Imageryhttp://academiccommons.columbia.edu/catalog/ac:177050
Liu, Xin; Imielinska, Celina Z.; Rosiene, Joel; Connolly Jr., E. Sander; D'Ambrosio, Anthony L.http://dx.doi.org/10.7916/D80C4T8VTue, 09 Sep 2014 00:00:00 +0000We present an automated generic methodology for symmetry identification and asymmetry quantification, novel method of identifying and delineation of brain pathology by analyzing the opposing sides of the brain utilizing of inherent leftright symmetry in the brain. After symmetry axis has been detected, we apply non-parametric statistical tests operating on the pairs of samples to identify initial seeds points which is defined defined as the pixels where the most statistically significant difference appears. Local region growing is performed on the difference map, from where the seeds are aggregating until it captures all 8-way connected high signals from the difference map. We illustrate the capability of our method with examples ranging from tumors in patient MR data to animal stroke data. The validation results on Rat stroke data have shown that this approach has promise to achieve high precision and full automation in segmenting lesions in reflectional symmetrical objects.Bioinformatics, Neurosciences, Medical imaging and radiologyci42, esc2181Neurological Surgery, Radiation Oncology, Biomedical Informatics, Computer ScienceConferencesQuantification of Diffusion-weighted Images (DWI) and Apparent Diffusion Coefficient Maps (ADC) in the Detection of Acute Strokehttp://academiccommons.columbia.edu/catalog/ac:177054
Tulipano, Paola K.; Millar, William S.; Imielinska, Celina Z.; Liu, Xin; Rosiene, Joel; D'Ambrosio, Anthony L.http://dx.doi.org/10.7916/D8DJ5D4XTue, 09 Sep 2014 00:00:00 +0000Magnetic resonance (MR) imaging is an imaging modality that is used in the management and diagnosis of acute stroke. Common MR imaging techniques such as diffusion weighted imaging (DWI) and apparent diffusion coefficient maps (ADC) are used routinely in the diagnosis of acute infarcts. However, advances in radiology information systems and imaging protocols have led to an overload of image information that can be difficult to manage and time consuming. Automated techniques to assist in the identification of acute ischemic stroke can prove beneficial to 1) the physician by providing a mechanism for early detection and 2) the patient by providing effective stroke therapy at an early stage. We have processed DW images and ADC maps using a novel automated Relative Difference Map (RDM) method that was tailored to the identification and delineation of the stroke region. Results indicate that the technique can delineate regions of acute infarctions on DW images and ADC maps. A formal evaluation of the RDM algorithm was performed by comparing accuracy measurementsbetween 1) expert generated ground truths with the RDM delineated DWI infarcts and 2) RDM delineated DWI infarcts with RDM delineated ADC infarcts. The accuracy measurements indicate that the RDM delineated DWI infarcts are comparable to the expert generated ground truths. The true positive volume fraction value (TPVF), between RDM delineated DWI and ADC infarcts, is nonzero for all cases with an acute infarct while the value for non-acute cases remains zero.Bioinformatics, Medical imaging and radiology, Biomedical engineeringpkt2, wsm8, ci42Radiation Oncology, Biomedical Informatics, Computer Science, RadiologyConferencesStatistical Bilateral Asymmetry Measurement in Brain Imageshttp://academiccommons.columbia.edu/catalog/ac:177036
Liu, Xin; Ogden, Robert T.; Imielinska, Celina Z.; Laine, Andrew F.; Connolly Jr., E. Sander; D'Ambrosio, Anthonyhttp://dx.doi.org/10.7916/D88W3BS2Tue, 09 Sep 2014 00:00:00 +0000We present an improvement of an automated generic methodology for symmetry identification, asymmetry quantification, and segmentation of brain pathologies, utilizing the inherent bi-fold mirror symmetry in brain imagery. In the pipeline of operations starting with detection of the symmetry axis, hemisphere-wise cross registration, statistical correlation and quantification of asymmetries, we segment a target brain pathology. The detection of pathological difference left to right in brain imagery is complicated by normal variations as well as geometric misalignment in anatomical structures between two hemispheres. Introducing hemisphere-wise registration and spatial correlation makes our approach perform robustly in the presence of normal asymmetries and systematic artifacts such as bias field and acquisition noise.Medical imaging and radiology, Biomedical engineering, Bioinformaticsxl2104, to166, ci42, al418, esc2181, ad3197Radiation Oncology, Neurological Surgery, Biomedical Informatics, Computer Science, Biostatistics, Biomedical EngineeringConferencesAutomatic Correction of the 3D Orientation of the Brain Imageryhttp://academiccommons.columbia.edu/catalog/ac:177039
Liu, Xin; Imielinska, Celina Z.; Connolly Jr., E. Sander; D'Ambrosio, Anthonyhttp://dx.doi.org/10.7916/D81C1VBBTue, 09 Sep 2014 00:00:00 +0000Classification of human brain pathologies can be guided by the estimation of the departure of 3D internal structures from the normal bilateral symmetry. However symmetry based analysis can 't be precisely carried out when the 3D brain orientation is misaligned, a common occurrence in clinical practice. In this paper, a technique to automatically identify the symmetry plane and correct the 3D orientation of volumetric brain images in a cost effective way is developed. The algorithm seeks the best sampling strategies to realign 3D volumetric representation of the brain within scanner coordinate system. The inertia matrix is computed on the sampled brain, and the principle axes are derived from the eigen vectors of the inertia matrix. The technique is demonstrated on MR and CT brain images and the detected symmetry plane that is orthogonal to the principle vectors is provided. A spatial affine transform is applied to rotate the 3D brain images and align them within the coordinate system of the scanner. The corrected brain volume is re-sliced such that each planar image represents the brain at the same axial level.Medical imaging and radiology, Biomedical engineering, Bioinformaticsxl2104, ci42, esc2181, ad3197Neurological Surgery, Radiation Oncology, Biomedical Informatics, Computer ScienceConferencesMulti-scale Modeling of Trauma Injuryhttp://academiccommons.columbia.edu/catalog/ac:177003
Imielinska, Celina Z.; Przekwas, Andrzej; Tan, X. G.http://dx.doi.org/10.7916/D8XK8D1QTue, 09 Sep 2014 00:00:00 +0000We develop a multi-scale high fidelity biomechanical and physiologically-based modeling tools for trauma (ballistic/impact and blast) injury to brain, lung and spinal cord for resuscitation, treatment planning and design of personnel protection. Several approaches have been used to study blast and ballistic/impact injuries. Dummy containing pressure sensors and synthetic phantoms of human organs have been used to study bomb blast and car crashes. Large animals like pigs also have been equipped with pressure sensors exposed to blast waves. But these methods do not anatomically and physiologically biofidelic to humans, do not provide full optimization of body protection design and require animal sacrifice. Anatomy and medical image based high-fidelity computational modeling can be used to analyze injury mechanisms and to optimize the design of body protection. This paper presents novel approach of coupled computational fluid dynamics (CFD) and computational structures dynamics (CSD) to simulate fluid (air, cerebrospinal fluid) solid (cranium, brain tissue) interaction during ballistic/blast impact. We propose a trauma injury simulation pipeline concept staring from anatomy and medical image based high fidelity 3D geometric modeling, extraction of tissue morphology, generation of computational grids, multiscale biomechanical and physiological simulations, and data visualization.Medical imaging and radiology, Biomedical engineering, Bioinformaticsci42Radiation Oncology, Biomedical Informatics, Computer ScienceArticlesGlobal gene expression analyses of bystander and alpha particle irradiated normal human lung fibroblasts: Synchronous and differential responseshttp://academiccommons.columbia.edu/catalog/ac:185168
Ghandhi, Shanaz; Yaghoubian, Benjamin; Amundson, Sally A.http://dx.doi.org/10.7916/D8PN942RMon, 08 Sep 2014 00:00:00 +0000The existence of a radiation bystander effect, in which non-irradiated cells respond to signals from irradiated cells, is now well established. It raises concerns for the interpretation of risks arising from exposure to low doses of ionizing radiation. However, the regulatory mechanisms involved in the bystander response have not been well elucidated. To provide insight into the signaling pathways responding in bystanders, we have measured global gene expression four hours after bystander and direct alpha particle exposure of primary human lung fibroblasts. Although common p53-regulated radiation response genes like CDKN1A were expressed at elevated levels in the directly exposed cultures, they showed little or no change in the bystanders. In contrast, genes regulated by NFκB, such as PTGS2 (cyclooxygenase-2), IL8 and BCL2A1, responded nearly identically in bystander and irradiated cells. This trend was substantiated by gene ontology and pathway analyses of the microarray data, which suggest that bystander cells mount a full NFκB response, but a muted or partial p53 response. In time-course analyses, quantitative real-time PCR measurements of CDKN1A showed the expected 4-hour peak of expression in irradiated but not bystander cells. In contrast, PTGS2, IL8 and BCL2A1 responded with two waves of expression in both bystander and directly irradiated cells, one peaking at half an hour and the other between four and six hours after irradiation. Two major transcriptional hubs that regulate the direct response to ionizing radiation are also implicated in regulation of the bystander response, but to dramatically different degrees. While activation of the p53 response pathway is minimal in bystander cells, the NFκB response is virtually identical in irradiated and bystander cells. This alteration in the balance of signaling is likely to lead to different outcomes in irradiated cells and their bystanders, perhaps leading to greater survival of bystanders and increased risk from any long-term damage they have sustained.Medical imaging and radiology, Geneticssg2423, saa2108Radiation Oncology, Center for Radiological ResearchArticlesMechanisms of increased risk of tumorigenesis in Atm and Brca1 double heterozygosityhttp://academiccommons.columbia.edu/catalog/ac:183114
Wang, Jufang; Su, Fengtao; Smilenov, Lubomir B.; Zhou, Libin; Hu, Wentao; Ding, Nan; Zhou, Guangminghttp://dx.doi.org/10.7916/D8C24TSWMon, 08 Sep 2014 00:00:00 +0000Both epidemiological and experimental studies suggest that heterozygosity for a single gene is linked with tumorigenesis and heterozygosity for two genes increases the risk of tumor incidence. Our previous work has demonstrated that Atm/Brca1 double heterozygosity leads to higher cell transformation rate than single heterozygosity. However, the underlying mechanisms have not been fully understood yet. In the present study, a series of pathways were investigated to clarify the possible mechanisms of increased risk of tumorigenesis in Atm and Brca1 heterozygosity. Wild type cells, Atm or Brca1 single heterozygous cells, and Atm/Brca1 double heterozygous cells were used to investigate DNA damage and repair, cell cycle, micronuclei, and cell transformation after photon irradiation. Remarkable high transformation frequency was confirmed in Atm/Brca1 double heterozygous cells compared to wild type cells. It was observed that delayed DNA damage recognition, disturbed cell cycle checkpoint, incomplete DNA repair, and increased genomic instability were involved in the biological networks. Haploinsufficiency of either ATM or BRCA1 negatively impacts these pathways. The quantity of critical proteins such as ATM and BRCA1 plays an important role in determination of the fate of cells exposed to ionizing radiation and double heterozygosity increases the risk of tumorigenesis. These findings also benefit understanding of the individual susceptibility to tumor initiation.Medical imaging and radiologylbs5Radiation OncologyArticlesMulti-Scale Visual Analysis of Trauma Injuryhttp://academiccommons.columbia.edu/catalog/ac:151498
Imielinska, Celina Z.; Przekwas, Andrzej; Tan, X. G.http://hdl.handle.net/10022/AC:P:14345Mon, 13 Aug 2012 00:00:00 +0000We develop a multi-scale high-fidelity biomechanical and physiologically based modeling tools for trauma (ballistic/impact and blast) injury to brain, lung and spinal cord for resuscitation, treatment planning and design of personnel protection. Several approaches have been used to study blast and ballistic/impact injuries. Dummy containing pressure sensors and synthetic phantoms of human organs have been used to study bomb blast and car crashes. Large animals like pigs also have been equipped with pressure sensors exposed to blast waves. But these methods do not provide anatomically and physiologically, full optimization of body protection design and require animal sacrifice. Anatomy and medical image-based high-fidelity computational modeling can be used to analyze injury mechanisms and to optimize the design of body protection. This paper presents novel approach of coupled computational fluid dynamics and computational structures dynamics to simulate fluid (air, cerebrospinal fluid)–solid (cranium, brain tissue) interaction during ballistic/blast impact. We propose a trauma injury simulation pipeline concept staring from anatomy and medical image-based high-fidelity 3D geometric modeling, extraction of tissue morphology, generation of computational grids, multi-scale biomechanical and physiological simulations, and data visualization.Biomedical informatics, Medical imaging and radiologyci42Radiation OncologyArticlesIncorporating 3D virtual anatomy into the medical curriculumhttp://academiccommons.columbia.edu/catalog/ac:151515
Imielinska, Celina Z.; Molholt, Pat A.http://hdl.handle.net/10022/AC:P:14349Mon, 13 Aug 2012 00:00:00 +0000The introduction of the Visible Human Project by Ackerman in 1995, described in the seminal paper in 1996, brought a promise to anatomists that these two frozen, milled, and digitized cadavers--the Visible Male and Female--would revolutionize anatomy teaching by providing the most complete and detailed anatomical images ever. This vision could be compared to the proverbial "man on the moon" program for medical education and has proven to be much more challenging than expected. Although the ramifications of this project are not of the same scale as the shock created five centuries ago by the Padua physician Andreas Vesalius when he challenged the ancient Greek physician Galen's description of the human body, the original interest created by the availability of the Visible Human data was enormous.Science education, Medical imaging and radiologyci42, pm38Radiation Oncology, Biomedical InformaticsArticlesEvaluation of automated segmentation of hip joint in revision arthroplastyhttp://academiccommons.columbia.edu/catalog/ac:151501
Domanski, J.; Imielinska, Celina Z.; Skalski, K.; Kwiatkowski, K.; Sowinski, T.http://hdl.handle.net/10022/AC:P:14346Mon, 13 Aug 2012 00:00:00 +0000We present a case of a 72-year-old female patient with a history of degenerative hip joint disease for whom a custom-made prosthesis—an acetabulum cage—was designed. With the growing number of total hip arthroplasty (THA) operations and the rapid development of technology, biology, and tissue bioengineering, there is a market to develop new artificial hip joints. The quality of the custom made prosthesis depends on the quality of segmentation to delineate accurately patient’s anatomy. The error of segmentation may propagate to the overall error of the final prosthesis. We evaluate an in-house segmentation method, that was used in the design of the custom made prosthesis, and a commercial segmentation method, using qualitative and quantitative approaches.Medical imaging and radiologyci42Radiation OncologyArticlesA framework for evaluating image segmentation algorithmshttp://academiccommons.columbia.edu/catalog/ac:151518
Udupa, Jayaram K.; LeBlanc, Vicki R.; Zhuge, Ying; Imielinska, Celina Z.; Schmidt, Hilary; Currie, Leanne M.; Hirsch, Bruce E.; Woodburn, Jameshttp://hdl.handle.net/10022/AC:P:14350Mon, 13 Aug 2012 00:00:00 +0000The purpose of this paper is to describe a framework for evaluating image segmentation algorithms. Image segmentation consists of object recognition and delineation. For evaluating segmentation methods, three factors—precision (reliability), accuracy (validity), and efficiency (viability)—need to be considered for both recognition and delineation. To assess precision, we need to choose a figure of merit, repeat segmentation considering all sources of variation, and determine variations in figure of merit via statistical analysis. It is impossible usually to establish true segmentation. Hence, to assess accuracy, we need to choose a surrogate of true segmentation and proceed as for precision. In determining accuracy, it may be important to consider different 'landmark' areas of the structure to be segmented depending on the application. To assess efficiency, both the computational and the user time required for algorithm training and for algorithm execution should be measured and analyzed. Precision, accuracy, and efficiency factors have an influence on one another. It is difficult to improve one factor without affecting others. Segmentation methods must be compared based on all three factors, as illustrated in an example wherein two methods are compared in a particular application domain. The weight given to each factor depends on application.Medical imaging and radiologyci42Radiation Oncology, Nursing, Center for Education Research and EvaluationArticlesAsymmetry Analysis in Rodent Cerebral Ischemia Modelshttp://academiccommons.columbia.edu/catalog/ac:151509
Liu, Sheena Xin; Imielinska, Celina Z.; Laine, Andrew F.; Millar, William S.; Connolly, Edward S.; D'Ambrosio, Anthony L.http://hdl.handle.net/10022/AC:P:14348Mon, 13 Aug 2012 00:00:00 +0000Rationale and Objectives: An automated method for identification and segmentation of acute/subacute ischemic stroke, using the inherent bi-fold symmetry in brain images, is presented. An accurate and automated method for localization of acute ischemic stroke could provide physicians with a mechanism for early detection and potentially faster delivery of effective stroke therapy. Materials and Methods: Segmentation of ischemic stroke was performed on magnetic resonance (MR) images of subacute rodent cerebral ischemia. Eight adult male Wistar rats weighing 225–300 g were anesthetized with halothane in a mix of 70% nitrous oxide/30% oxygen. Animal core temperature was maintained at 37°C during the entire surgical procedure, including occlusion of the middle cerebral artery (MCA) and the 90-minute post-reperfusion period. To confirm cerebral ischemia, transcranial measurements of cerebral blood flow were performed with laser-Doppler flowmetry, using 15-mm flexible fiberoptic Doppler probes attached to the skull over the MCA territory. Animal MR scans were performed at 1.5 T using a knee coil. Three experts performed manual tracing of the stroke regions for each rat, using the histologic-stained slices to guide delineation of stroke regions. A strict tracing protocol was followed that included multiple (three) tracings of each stroke region. The volumetric MR image data were processed for each rat by computing the axis of symmetry and extracting statistical dissimilarities. A nonparametric Wilcoxon rank sum test operating on paired windows in opposing hemispheres identified seeds in the pixels exhibiting statistically significant bi-fold mirror asymmetry. Two brain reference maps were used for analysis: an absolute difference map (ADM) and a statistical difference map (SDM). Although an ADM simply displays the absolute difference by subtracting one brain hemisphere from its reflection, SDM highlights regions by labeling pixels exhibiting statistically significant asymmetry. Results: To assess the accuracy of the proposed segmentation method, the surrogate ground truth (the stroke tracing data) was compared to the results of our proposed automated segmentation algorithm. Three accuracy segmentation metrics were utilized: true-positive volume fraction (TPVF), false-positive volume fraction (FPVF), and false-negative volume fraction (FNVF). The mean value of the TPVF for our segmentation method was 0.8877; 95% CI 0.7254 to 1.0500; the mean FPVF was 0.3370, 95% CI –0.0893 to 0.7633; the mean FNVF was 0.1122, 95% CI –0.0502 to 0.2747. Conclusions: Unlike most segmentation methods that require some degree of manual intervention, our segmentation algorithm is fully automated and highly accurate in identifying regions of brain asymmetry. This approach is attractive for numerous neurologic applications where the operator's intervention should be minimal or null.Medical imaging and radiology, Neurosciencesxl2104, ci42, al418, wsm8, esc5Neurological Surgery, Radiation Oncology, Biomedical Informatics, Radiology, Biomedical EngineeringArticlesToward Objective Quantification of Perfusion-weighted Computed Tomography in Subarachnoid Hemorrhage: Quantification of Symmetry and Automated Delineation of Vascular Territorieshttp://academiccommons.columbia.edu/catalog/ac:151504
Imielinska, Celina Z.; Liu, Sheena Xin; Rosiene, Joel; Sughrue, Michael E.; Mocco, J.; Komotar, Ricardo J.; Ransom, Evan R.; Lignelli-Dipple, Angela; Zacharia, Brad E.; Connolly, Edward S.; D'Ambrosio, Anthony L.http://hdl.handle.net/10022/AC:P:14347Mon, 13 Aug 2012 00:00:00 +0000Rationale and Objectives: Perfusion-weighted computed tomography (CTP) is a relatively recent innovation that estimates a value for cerebral blood flow (CBF) using a series of axial head CT images tracking the time course of a signal from an intravenous contrast bolus. Materials and Methods: CTP images were obtained using a standard imaging protocol and were analyzed using commercially available software. A novel computer-based method was used for objective quantification of side-to-side asymmetries of CBF values calculated from CTP images. Results: Our method corrects for the inherent variability of the CTP methodology seen in the subarachnoid hemorrhage (SAH) patient population to potentially aid in the diagnosis of cerebral vasospasm (CVS). This method analyzes and quantifies side-to-side asymmetry of CBF and presents relative differences in a construct termed a Relative Difference Map (RDM). To further automate this process, we have developed a unique methodology that enables a computer to delineate vascular territories within a brain image, regardless of the size and shape of the brain. Conclusions: While both the quantification of image symmetry using RDMs and the automated assignment of vascular territories were initially designed for the analysis of CTP images, it is likely that they will be useful in a variety of applications.Medical imaging and radiologyci42, xl2104, al270, bez2103, esc5Neurological Surgery, Radiation Oncology, Biomedical Informatics, Radiology, BiostatisticsArticlesNew views of male pelvic anatomy: Role of computer-generated 3D imageshttp://academiccommons.columbia.edu/catalog/ac:151521
Venuti, Judith M.; Imielinska, Celina Z.; Molholt, Pat A.http://hdl.handle.net/10022/AC:P:14351Mon, 13 Aug 2012 00:00:00 +0000There is considerable controversy concerning the role of cadaveric dissection in teaching gross anatomy and the potential of using 3D computer-generated images to substitute for actual laboratory dissections. There are currently few high-quality 3D virtual models of anatomy available to evaluate the utility of computer-generated images. Existing 3D models are frequently of structures that are easily examined in three dimensions by removal from the cadaver, i.e., the heart, skull, and brain. We have focused on developing a 3D model of the pelvis, a region that is conceptually difficult and relatively inaccessible for student dissection. We feel students will benefit tremendously from 3D views of the pelvic anatomy. We generated 3D models of the male pelvic anatomy from hand-segmented color Visible Human Male cryosection data, reconstructed and visualized by Columbia University's in-house 3D Vesalius Visualizer.1 These 3D models depict the anatomy of the region in a realistic true-to-life color and texture. They can be used to create 3D anatomical scenes, with arbitrary complexity, where the component anatomical structures are displayed in correct 3D anatomical relationships. Moreover, a sequence of 3D scenes can be defined to simulate actual dissection. Structures can be added in a layered sequence from the bony framework to build from the "inside-out" or disassembled much like a true laboratory dissection from the "outside-in." These 3D reconstructed anatomical models can provide views of the structures from new perspectives and have the potential to improve understanding of the anatomical relationships of the pelvic region (http://www.cellbiology.lsuhsc.edu/People/Faculty/Venuti_Figures/movie_index.html).Medical imaging and radiologyci42, pm38Radiation Oncology, Biomedical Informatics, Pathology and Cell BiologyArticlesA General Approach to Model Biomedical Data from 3D Unorganised Point Clouds with Medial Scaffoldshttp://academiccommons.columbia.edu/catalog/ac:151536
Leymarie, Frederic Fol; Imielinska, Celina Z.; Chang, Ming-Ching; Kimia, Benjamin B.http://hdl.handle.net/10022/AC:P:14356Mon, 13 Aug 2012 00:00:00 +0000We present the latest developments in modeling 3D biomedical data via the Medial Scaffold (MS), a 3D acyclic oriented graph representation of the Medial Axis (MA) [LK07, SP08]. The MS (and associated 3DMA) can be computed as the result of the singularities of a geometric wave propagation simulation. We consider here some of the potential applications of this shape model in the realm of biomedical imaging. We can reconstruct complex object surfaces and make explicit the coarse-scale structures, which are ready-to-use in a number of practical applications, including: morphological measurement for cortex or bone thickness, centerline extraction (curve skeleton) for tracheotomy or colonoscopy, surface partitioning for cortical or anatomical surface classification, as well as registration and matching of shapes of tumors or carpal bones. The MS permits to automatically and efficiently map an unorganised point cloud, i.e., simple 3D coordinates of point samples, to a coherent surface set and associated approximate MA. The derived MS is used to further recover significant medium and large scale features, such as surface ridges and main axial symmetries. The radius field of the MS provides an intuitive definition for morphological measurements, while the graph structure made explicit by the MS is useful for shape registration and matching applications.Medical imaging and radiology, Computer scienceci42Radiation OncologyArticlesModeling Real-Time 3-D Lung Deformations for Medical Visualizationhttp://academiccommons.columbia.edu/catalog/ac:151524
Santhanam, Anand P.; Imielinska, Celina Z.; Davenport, Paul; Kupelian, Patrick; Rolland, Jannick P.http://hdl.handle.net/10022/AC:P:14352Mon, 13 Aug 2012 00:00:00 +0000In this paper, we propose a physics-based and physiology-based approach for modeling real-time deformations of 3-D high-resolution polygonal lung models obtained from high-resolution computed tomography (HRCT) images of normal human subjects. The physics-based deformation operator is nonsymmetric, which accounts for the heterogeneous elastic properties of the lung tissue and spatial-dynamic flow properties of the air. An iterative approach is used to estimate the deformation with the deformation operator initialized based on the regional alveolar expandability, a key physiology-based parameter. The force applied on each surface node is based on the airflow pattern inside the lungs, which is known to be based on the orientation of the human subject. The validation of lung dynamics is done by resimulating the lung deformation and comparing it with HRCT data and computing force applied on each node derived from a 4-D HRCT dataset of a normal human subject using the proposed deformation operator and verifying its gradient with the orientation.Medical imaging and radiologyci42Radiation OncologyArticlesEmploying Symmetry Features for Automatic Misalignment Correction in Neuroimageshttp://academiccommons.columbia.edu/catalog/ac:151530
Liu, Sheena Xin; Kender, John R.; Imielinska, Celina Z.; Laine, Andrew F.http://hdl.handle.net/10022/AC:P:14354Mon, 13 Aug 2012 00:00:00 +0000A novel method to automatically compute the symmetry plane and to correct the 3D orientation of neuro-images is presented. In acquisition of neuroimaging scans, the lack of perfect alignment of a patient's head makes it challenging to evaluate brain images. By deploying a shape-based criterion, the symmetry plane is defined as a plane that best matches external surface points on one side of the head, with their counterparts on the other side. In our method, the head volume is represented as a re-parameterized surface point cloud, where each location is parameterized by its elevation (latitude), azimuth (longitude), and radius. The search for the best matching surfaces is implemented in a multi-resolution paradigm, and the computation time is significantly decreased. The algorithm was quantitatively evaluated using in both simulated data and in real T1, T2, Flair magnetic resonance patient images. This algorithm is found to be fast (< 10s per MR volume), robust and accurate (< .6 degree of Mean Angular Error), invariant to the acquisition noise, slice thickness, bias field, and pathological asymmetries.Medical imaging and radiology, Neurosciencesxl2104, jrk3, ci42, al418Radiation Oncology, Computer Science, Radiology, Biomedical EngineeringArticlesPost-carotid endarterectomy neurocognitive decline is associated with cerebral blood flow asymmetry on post-operative magnetic resonance perfusion brain scanshttp://academiccommons.columbia.edu/catalog/ac:151527
Wilson, David A.; Mocco, J.; D'Ambrosio, Anthony L.; Komotar, Ricardo J.; Zurica, Joseph; Kellner, Christopher; Hahn, David K.; Connolly, Edward S.; Liu, Sheena Xin; Imielinska, Celina Z.; Heyer, Eric J.http://hdl.handle.net/10022/AC:P:14353Mon, 13 Aug 2012 00:00:00 +0000Objective: Up to 25% of patients experience subtle declines in post-operative neurocognitive function following, otherwise uncomplicated, carotid endarterectomy (CEA). We sought to determine if post-CEA neurocognitive deficits are associated with cerebral blood flow (CBF) abnormalities on post-operative MR perfusion brain scans. Methods: We enrolled 22 CEA patients to undergo a battery of neuropsychometric tests pre-operatively and on post-operative day 1 (POD 1). Neurocognitive dysfunction was defined as a two standard deviation decline in performance in comparison to a similarly aged control group of lumbar laminectomy patients. All patients received MR perfusion brain scans on POD 1 that were analysed for asymmetries in CBF distribution. One patient experienced a transient ischemic attack within 24 hours before the procedure and was excluded from our analysis. Results: Twenty-nine percent of CEA patients demonstrated neurocognitive dysfunction on POD 1. One hundred percent of those patients with cognitive deficits demonstrated CBF asymmetry, in contrast to only 27% of those patients without cognitive impairment. Post-CEA cognitive dysfunction was significantly associated with CBF abnormalities (RR=3.75, 95% CI: 1.62-8.67, p=0.004). Conclusion: Post-CEA neurocognitive dysfunction is significantly associated with post-operative CBF asymmetry. These results support the hypothesis that post-CEA cognitive impairment is caused by cerebral hemodynamic changes. Further work exploring the relationship between CBF and post-CEA cognitive dysfunction is needed.Medical imaging and radiology, Neurosciencescpk2103, esc5, xl2104, ci42, ejh3Neurological Surgery, Radiation Oncology, Biomedical Informatics, Anesthesiology, NeurologyArticlesAutomatic Misalignment Correction in Neuroimages Using Surface Symmetry Priorshttp://academiccommons.columbia.edu/catalog/ac:151533
Liu, Sheena Xin; Kender, John R.; Imielinska, Celina Z.; Laine, Andrew F.http://hdl.handle.net/10022/AC:P:14355Mon, 13 Aug 2012 00:00:00 +0000Many brain imaging procedures require the careful alignment of different sets of images obtained in the same individual. The available automatic methods for brain alignment are susceptible to improvement. This paper discusses briefly a new automatic method to reinstall the tilted orientation of head images, using surface symmetry as a prior.Medical imaging and radiology, Neurosciencesxl2104, jrk3, ci42, al418Radiation Oncology, Computer Science, Radiology, Biomedical EngineeringArticles